we have replicated Arduino due design to one of our PoC board.
In that we are unable to load the program for USB to UART. let me know is any other way to do this.
From the DUE product page:
The Programming port is connected to an ATmega16U2, which provides a virtual COM port to software on a connected computer (To recognize the device, Windows machines will need a .inf file, but OSX and Linux machines will recognize the board as a COM port automatically). The 16U2 is also connected to the SAM3X hardware UART. Serial on pins RX0 and TX0 provides Serial-to-USB communication for programming the board through the ATmega16U2 microcontroller. The Arduino software includes a serial monitor which allows simple textual data to be sent to and from the board. The RX and TX LEDs on the board will flash when data is being transmitted via the ATmega16U2 chip and USB connection to the computer (but not for serial communication on pins 0 and 1).